In the proposed Phase II research, a commercially viable software reconstruction platform, employing the solution of the radiative transport equation (RTE), will be developed for accurate and robust in vivo imaging of fluorescent targets in small animals. Although small animal optical tomography systems have recently been introduced, current systems do not employ fluorescence or bioluminescence, which have been confined to planar projections. In addition, current optical tomography systems rely on the use of time independent measurements and reconstruction algorithms based on the diffusion approximation. However, it is well known that the small volumes and heterogeneities in mice present conditions where the diffusion approximation is not valid. Realizing this, transport based solutions of the RTE have been researched as a promising alternative. However, approaches to date have relied on numerical methods which do not have the accuracy or efficiency required for commercial deployment. In the Phase I research, Transpire's algorithms for solving the RTE were successfully applied towards a proof-of-concept process, employing BCM's expertise in frequency-domain photon migration (FPDM), for reconstruction of fluorophore concentrations in a 3-D mouse phantom. Phase II research will extend this work to develop an RTE based, tomographic reconstruction software platform for FDPM photon migration. The specific aims are: (1) to develop an optimized 3-D RTE solver for modeling excitation and emission light propagation in forward and adjoint modes, streamlined for small animal imaging conditions with non-contact, non-matching mediums; (2) to develop an adaptive non-linear algorithm employing forward and adjoint RTE solutions for fluorescence yield reconstructions in small animal volumes; (3) to enable hybrid microCT/optical imaging by developing automatic grid generation from microCT images; (4) to integrate the above components into an automated software system for FDPM tomographic reconstruction; and (5) to quantitative demonstrate commercial viability through imaging of a peptide targeted NIR and visible fluorescent contrast agent in xenograft mice. Successful completion of Phase II will result in an automated software product, when combined with BCM's expertise in hardware technologies for frequency-domain fluorescence small animal imaging, can result in a commercially viable small animal imaging system. The proposed Phase II research will substantially advance the state-of-the-art in optical small animal imaging, which could enhance drug discovery as well as contribute significantly to new understanding of disease processes. Through preclinical validation, the proposed research can ultimately be migrated towards clinical imaging in areas such as lymph node mapping and tumor margin definition in melanoma. [unreadable] [unreadable] [unreadable]